Research workbench
Crystal structure of broadly neutralizing antibody 3I14 bound to the influenza a H10 hemagglutinin
Analyse Crystal structure of broadly neutralizing antibody 3I14 bound to the influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WF1
- Type
- protein
- Length
- 922 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Hemagglutinin HA2 chain; Heavy chain; Light chain
- UniProt
- A0A0J9X252, A0A0J9X253
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 318 | 9% helix, 38% strand | A0A0J9X252 |
| B | Hemagglutinin HA2 chain | protein | 171 | 54% helix, 12% strand | A0A0J9X253 |
| H | Heavy chain | protein | 222 | 4% helix, 43% strand | — |
| L | Light chain | protein | 211 | 5% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.77 | 0.91 | 33 | empty |
| 2 | 189 | 0.65 | 0.84 | 28 | empty |
| 3 | 322 | 0.60 | 0.78 | 33 | empty |
| 4 | 514 | 0.60 | 0.74 | 65 | empty |
| 5 | 294 | 0.53 | 0.75 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3111 Ų buried · 30 hydrogen bonds · protein-protein
- H–L · 1747 Ų buried · 6 hydrogen bonds · protein-protein
- B–H · 462 Ų buried · 3 hydrogen bonds · protein-protein
- B–L · 334 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 96 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6WF1 · Crystal Structure of Broadly Neutralizing Antibody 3I14 Bound to the Influenza A H10… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A0J9X252
- Every structure of UniProt A0A0J9X253
- Elsewhere: RCSB PDB 6WF1 · PDBe 6WF1 · UniProt A0A0J9X252 · UniProt A0A0J9X253
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